This invention relates to the manufacture of supports or substrates having bound to the surfaces thereof a plurality of chemical compounds, such as biopolymers. In particular, the invention relates to the manufacture of microarray slides of non-standard size and, more particularly, to the manufacture of microarray slides having a size that is smaller in at least one dimension than a standard microscopic slide.
In the field of diagnostics and therapeutics, it is often useful to attach species to a surface. One important application is in solid phase chemical synthesis wherein initial derivatization of a substrate surface enables synthesis of polymers such as oligonucleotides and peptides on the substrate itself. Support bound oligomer arrays, particularly oligonucleotide arrays, may be used in screening studies for determination of binding affinity.
Determining the nucleotide sequences and expression levels of nucleic acids (DNA and RNA) is critical to understanding the function and control of genes and their relationship, for example, to disease discovery and disease management. Analysis of genetic information plays a crucial role in biological experimentation. This has become especially true with regard to studies directed at understanding the fundamental genetic and environmental factors associated with disease and the effects of potential therapeutic agents on the cell. Such a determination permits the early detection of infectious organisms such as bacteria, viruses, etc.; genetic diseases such as sickle cell anemia; and various cancers. This paradigm shift has lead to an increasing need within the life science industries for more sensitive, more accurate and higher-throughput technologies for performing analysis on genetic material obtained from a variety of biological sources.
Unique or misexpressed nucleotide sequences in a polynucleotide can be detected by hybridization with a nucleotide multimer, or oligonucleotide, probe. Hybridization is based on complementary base pairing. When complementary single stranded nucleic acids are incubated together, the complementary base sequences bind to one another or pair to form double stranded hybrid molecules. These techniques rely upon the inherent ability of nucleic acids to form duplexes via hydrogen bonding according to Watson-Crick base-pairing rules. The ability of single stranded deoxyribonucleic acid (ssDNA) or ribonucleic acid (RNA) to form a hydrogen bonded structure with a complementary nucleic acid sequence has been employed as an analytical tool in molecular biology research. An oligonucleotide probe employed in the detection is selected with a nucleotide sequence complementary, usually exactly complementary, to the nucleotide sequence in the target nucleic acid. Following hybridization of the probe with the target nucleic acid, any oligonucleotide probe/nucleic acid hybrids that have formed are typically separated from unhybridized probe. The amount of oligonucleotide probe in either of the two separated media is then tested to provide a qualitative or quantitative measurement of the amount of target nucleic acid originally present.
Direct detection of labeled target nucleic acid hybridized to surface-bound polynucleotide probes is particularly advantageous if the surface contains a mosaic of different probes that are individually localized to discrete, and often known, areas of the surface. Such ordered arrays containing a large number of oligonucleotide probes have been developed as tools for high throughput analyses of genotype and gene expression. Oligonucleotides synthesized on a solid support recognize uniquely complementary nucleic acids by hybridization, and arrays can be designed to define specific target sequences, analyze gene expression patterns or identify specific allelic variations. The arrays may be used for conducting cell study, diagnosing disease, identifying gene expression, monitoring drug response, determination of viral load, identifying genetic polymorphisms, analyzing gene expression patterns or identifying specific allelic variations, and the like.
In one approach, cell matter is lysed, to release its DNA as fragments, which are then separated out by electrophoresis or other means, and then tagged with a fluorescent or other label. The resulting DNA mix is exposed to an array of oligonucleotide probes, whereupon selective binding to matching probe sites takes place. The array is then washed and interrogated to determine the extent of hybridization reactions. In one approach the array is imaged so as to reveal for analysis and interpretation the sites where binding has occurred. Arrays of different chemical compounds or moieties or probe species provide methods of highly parallel detection, and hence improved speed and efficiency, in assays. Assuming that the different sequence polynucleotides were correctly deposited in accordance with the predetermined configuration, then the observed binding is indicative of the presence and/or concentration of one or more polynucleotide components of the sample.
The arrays may be microarrays created on the surface of a support by in situ synthesis of biopolymers such as polynucleotides, polypeptides, polysaccharides, etc., and combinations thereof, or by deposition of molecules such as oligonucleotides, cDNA and so forth. In general, arrays are synthesized on a surface of a support or substrate by one of any number of synthetic techniques that are known in the art. In one approach, for example, the support may be one on which a single array of chemical compounds is synthesized. Alternatively, multiple arrays of chemical compounds may be synthesized on the support, which is then diced, i.e., cut, into individual assay devices, which are supports that each comprises a single array, or in some instances multiple arrays, on a surface of the support.
The dimensions of a standard microscope slide are generally about one inch (about 25 mm) in width, about three inches (about 75 mm) in length and about 0.040 inches (about 1 to 1.2 mm) in thickness. Many apparatus for automating various procedures that are employed in manipulations involving microarrays on slides are designed for the standard microscope slide. Such manipulations include contacting the surface of the slide with various reagents and washing buffers, providing for specific chemical conditions during which specific binding (e.g., hybridization) can occur or during which species-selective washing can occur, examining the surface for the results of contacting the surface with a sample, and so forth. Furthermore, many of the above known apparatus are designed assuming one array of chemical compounds per slide. A standard microscope slide can carry up to about 20,000 or more features comprising chemical compounds. In many circumstances much fewer features are required for analyzing samples for various analytes or components that might be present in the samples. For example, many determinations require only about 1500 to about 2500 features. This has given rise to having multiple arrays on the surface of a standard microscope slide. However, since many of the known apparatus are designed assuming one array per slide, standard microscope slides that have more than one array for conservation of samples and reagents, minimization of sample handling steps, and the like, usually include barriers for separating the arrays from one another during the processing and examining stages. The barriers may be physical such as, for example, ridges, gaskets, and the like, or chemical such as, for example, coatings that are hydrophobic, and the like. All of the above contribute to higher costs of manufacture and use.
There is, therefore, a need for methods of preparing slides with a single array of features where the slides are generally smaller than the standard microscope slide. There is also a need for methods and devices for using non-standard size slides with known equipment that is designed for handling a standard microscope slide in an automated manner. There is also a need for having one identifier associated with one array on a slide.